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Carex Siderosticta Plastid - Photosystem II

Title:

Carex Siderosticta Plastid - Photosystem II

Neugebauer, Tomasz ORCID: https://orcid.org/0000-0002-9743-5910 and Royer-Artuso, Nicolas (2016) Carex Siderosticta Plastid - Photosystem II. In: Art & Science Days 2016, June 1-4, 2016, Bourges, France.. (Unpublished)

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Text (Description of Sonification Method) (application/pdf)
ELEMENTS.pdf - Accepted Version
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Audio (MIDI for sense strand) (audio/midi)
sense-midi.mid
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Audio (MIDI for anti-sense strand) (audio/midi)
anti-sense-midi.mid
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Text (musical score for sense strand) (application/pdf)
sense.pdf
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Text (musical score for anti-sense strand) (application/pdf)
anti-sense.pdf
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Text (LilyPond for MIDI of anti-sense strand) (text/plain)
anti-sense-midi.ly
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Text (LilyPond for MIDI of sense strand) (text/plain)
sense-midi.ly
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Slideshow (Guest lecture to Electroacoustic Composition Class at Concordia University) (application/vnd.openxmlformats-officedocument.presentationml.presentation)
DNA Sonification.pptx
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Official URL: http://www.musinfo.fr/index.php/en/creation/art-sc...

Abstract

This composition is based on musical scores generated by software we developed that maps DNA sequences into musical notation. This particular example converts genes responsible for photosynthesis (photosystem II) found on the plastid of a carex siderosticta plant. We then had that score performed on two violins. We focused on the coding of the photosystem genes. However, the development of the software means that one could quickly convert any of the over 100 million individual sequences in GenBank into a musical score.
The software we developed parses FASTA nucleotide coding sequence files, and maps these into a musical composition. The algorithm maps each of the 20 amino acids onto specific pitches and each codon synonym onto duration for those pitches. The mapping is listed in Table 1. We used quartertones to be able to keep the results inside an octave. Rests at the end of a bar are added to create an 8/4 time signature – each amino acid note duration is based on which codon synonym appears in the sequence. The rests are added to avoid having to split notes across a bar. Our program writes out the results into two musical score files, one for the genes on each of the two strands of DNA. The resulting files use Lilypond format to express a musical score for the genes located on each strand of DNA. Finally, the open source Lilypond program is used to generate the PDF and MIDI files of the score and the two scores are played simultaneously.

Divisions:Concordia University > Library
Item Type:Conference or Workshop Item (Other)
Refereed:No
Authors:Neugebauer, Tomasz and Royer-Artuso, Nicolas
Date:June 2016
Digital Object Identifier (DOI):10.11573/spectrum.library.concordia.ca.00981471
Keywords:DNA sonification
ID Code:981471
Deposited By: TOMASZ NEUGEBAUER
Deposited On:09 Aug 2016 18:49
Last Modified:18 Jan 2018 17:53

References:

[1] Carex siderosticta plastid, complete genome. NCBI Reference Sequence: NC_027250.1. National
Center for Biotechnology Information, U.S. National Library of Medicine.
http://www.ncbi.nlm.nih.gov/nuccore/NC_027250.1

[2] LilyPond... music notation for everyone. http://lilypond.org/

[3] Susumu Ohno and Midori Ohno. The All Pervasive Principle of Repetitious Recurrence Governs Not
Only Coding Sequence Construction But Also Human Endeavor in Musical Composition. lmmunogenetics
24: 71-78, 1986. http://www.ncbi.nlm.nih.gov/pubmed/3744439

[4] John Dunn and Mary Anne Clark. Life Music: The Sonification of Proteins. Leonardo. February
1999, Vol. 32, No. 1, Pages 25-32.
http://www.mitpressjournals.org/doi/abs/10.1162/002409499552966#.Ve3ukNNViko
doi:10.1162/002409499552966

[5] Rie Takahashi and Jeffrey H Miller. Conversion of amino-acid sequence in proteins to classical
music: search for auditory patterns. Genome Biology. 2007, 8:405
doi:10.1186/gb-2007-8-5-405
http://genomebiology.com/2007/8/5/405
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